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mergin with branch beta

This commit is contained in:
Miriam Baglioni 2021-07-28 10:24:48 +02:00
parent 1a5b114906 825d9f0289
commit 6c936943aa
24 changed files with 449 additions and 326 deletions
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9
dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java
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@ -67,6 +67,7 @@ public class AuthorMerger {
a -> a
.getPid()
.stream()
.filter(Objects::nonNull)
.map(p -> new Tuple2<>(pidToComparableString(p), a)))
.collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1));
@ -78,6 +79,7 @@ public class AuthorMerger {
a -> a
.getPid()
.stream()
.filter(Objects::nonNull)
.filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p)))
.map(p -> new Tuple2<>(p, a)))
.collect(Collectors.toList());
@ -150,7 +152,7 @@ public class AuthorMerger {
}
private static boolean hasPid(Author a) {
if (a == null || a.getPid() == null || a.getPid().size() == 0)
if (a == null || a.getPid() == null || a.getPid().isEmpty())
return false;
return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue()));
}
@ -159,7 +161,10 @@ public class AuthorMerger {
if (StringUtils.isNotBlank(author.getSurname())) {
return new Person(author.getSurname() + ", " + author.getName(), false);
} else {
return new Person(author.getFullname(), false);
if (StringUtils.isNotBlank(author.getFullname()))
return new Person(author.getFullname(), false);
else
return new Person("", false);
}
}

2
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
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@ -98,7 +98,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
Result r = (Result) value;
if (Objects.nonNull(r.getTitle()) && r.getTitle().isEmpty()) {
if (Objects.isNull(r.getTitle()) || r.getTitle().isEmpty()) {
return false;
}

6
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala
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@ -367,7 +367,7 @@ object DataciteToOAFTransformation {
result.setDateofcollection(ISO8601FORMAT.format(d))
result.setDateoftransformation(ISO8601FORMAT.format(ts))
result.setDateoftransformation(ISO8601FORMAT.format(d))
result.setDataInfo(dataInfo)
val creators = (json \\ "creators").extractOrElse[List[CreatorType]](List())
@ -532,11 +532,11 @@ object DataciteToOAFTransformation {
JField("awardUri", JString(awardUri)) <- fundingReferences
} yield awardUri
result.setId(IdentifierFactory.createIdentifier(result))
var relations: List[Relation] = awardUris.flatMap(a => get_projectRelation(a, result.getId)).filter(r => r != null)
fix_figshare(result)
result.setId(IdentifierFactory.createIdentifier(result))
if (result.getId == null)
return List()

2
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml
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@ -16,7 +16,7 @@
</parameters>
<start to="TransformJob"/>
<start to="ImportDatacite"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>

15
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala
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@ -3,13 +3,14 @@ package eu.dnetlib.dhp.actionmanager.datacite
import com.fasterxml.jackson.databind.ObjectMapper
import com.fasterxml.jackson.databind.SerializationFeature
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
import eu.dnetlib.dhp.schema.oaf.Oaf
import org.junit.jupiter.api.extension.ExtendWith
import org.junit.jupiter.api.{BeforeEach, Test}
import org.mockito.junit.jupiter.MockitoExtension
import java.text.SimpleDateFormat
import java.util.Locale
import scala.io.Source
@ExtendWith(Array(classOf[MockitoExtension]))
@ -22,6 +23,18 @@ class DataciteToOAFTest extends AbstractVocabularyTest{
super.setUpVocabulary()
}
@Test
def testDateMapping:Unit = {
val inputDate = "2021-07-14T11:52:54+0000"
val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US)
val dt = ISO8601FORMAT.parse(inputDate)
println(dt.getTime)
}
@Test
def testMapping() :Unit = {
val record =Source.fromInputStream(getClass.getResourceAsStream("record.json")).mkString

2
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/record.json
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File diff suppressed because one or more lines are too long

3
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/GroupEntitiesSparkJob.java
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@ -38,7 +38,8 @@ import scala.Tuple2;
/**
* Groups the graph content by entity identifier to ensure ID uniqueness
*/
public class GroupEntitiesSparkJob {
public class
GroupEntitiesSparkJob {
private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class);

71
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java
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@ -23,6 +23,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
@ -77,48 +78,54 @@ public class SparkUpdateEntity extends AbstractSparkAction {
(type, clazz) -> {
final String outputPath = dedupGraphPath + "/" + type;
removeOutputDir(spark, outputPath);
final String ip = DedupUtility.createEntityPath(graphBasePath, type.toString());
if (HdfsSupport.exists(ip, sc.hadoopConfiguration())) {
JavaRDD<String> sourceEntity = sc
.textFile(DedupUtility.createEntityPath(graphBasePath, type.toString()));
JavaRDD<String> sourceEntity = sc
.textFile(DedupUtility.createEntityPath(graphBasePath, type.toString()));
if (mergeRelExists(workingPath, type.toString())) {
if (mergeRelExists(workingPath, type.toString())) {
final String mergeRelPath = DedupUtility
.createMergeRelPath(workingPath, "*", type.toString());
final String dedupRecordPath = DedupUtility
.createDedupRecordPath(workingPath, "*", type.toString());
final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, "*", type.toString());
final String dedupRecordPath = DedupUtility
.createDedupRecordPath(workingPath, "*", type.toString());
final Dataset<Relation> rel = spark
.read()
.load(mergeRelPath)
.as(Encoders.bean(Relation.class));
final Dataset<Relation> rel = spark.read().load(mergeRelPath).as(Encoders.bean(Relation.class));
final JavaPairRDD<String, String> mergedIds = rel
.where("relClass == 'merges'")
.where("source != target")
.select(rel.col("target"))
.distinct()
.toJavaRDD()
.mapToPair(
(PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(0), "d"));
final JavaPairRDD<String, String> mergedIds = rel
.where("relClass == 'merges'")
.where("source != target")
.select(rel.col("target"))
.distinct()
.toJavaRDD()
.mapToPair(
(PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(0), "d"));
JavaPairRDD<String, String> entitiesWithId = sourceEntity
.mapToPair(
(PairFunction<String, String, String>) s -> new Tuple2<>(
MapDocumentUtil.getJPathString(IDJSONPATH, s), s));
if (type == EntityType.organization) // exclude root records from organizations
entitiesWithId = excludeRootOrgs(entitiesWithId, rel);
JavaPairRDD<String, String> entitiesWithId = sourceEntity
.mapToPair(
(PairFunction<String, String, String>) s -> new Tuple2<>(
MapDocumentUtil.getJPathString(IDJSONPATH, s), s));
if (type == EntityType.organization) // exclude root records from organizations
entitiesWithId = excludeRootOrgs(entitiesWithId, rel);
JavaRDD<String> map = entitiesWithId
.leftOuterJoin(mergedIds)
.map(k -> {
if (k._2()._2().isPresent()) {
return updateDeletedByInference(k._2()._1(), clazz);
}
return k._2()._1();
});
JavaRDD<String> map = entitiesWithId
.leftOuterJoin(mergedIds)
.map(k -> {
if (k._2()._2().isPresent()) {
return updateDeletedByInference(k._2()._1(), clazz);
}
return k._2()._1();
});
sourceEntity = map.union(sc.textFile(dedupRecordPath));
sourceEntity = map.union(sc.textFile(dedupRecordPath));
}
sourceEntity.saveAsTextFile(outputPath, GzipCodec.class);
}
sourceEntity.saveAsTextFile(outputPath, GzipCodec.class);
});
}

42
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertDatasetToJsonRDD.scala Normal file
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@ -0,0 +1,42 @@
package eu.dnetlib.dhp.sx.graph
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, OtherResearchProduct, Publication, Result, Software, Dataset => OafDataset}
import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkConvertDatasetToJsonRDD {
def main(args: Array[String]): Unit = {
val log: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath")
val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath")
val resultObject = List("publication","dataset","software", "otherResearchProduct")
val mapper = new ObjectMapper()
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
resultObject.foreach{item =>
spark.read.load(s"$sourcePath/$item").as[Result].map(r=> mapper.writeValueAsString(r))(Encoders.STRING).rdd.saveAsTextFile(s"$targetPath/${item.toLowerCase}", classOf[GzipCodec])
}
}
}

67
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala Normal file
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@ -0,0 +1,67 @@
package eu.dnetlib.dhp.sx.graph
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset}
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkConvertRDDtoDataset {
def main(args: Array[String]): Unit = {
val log: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath")
val t = parser.get("targetPath")
log.info(s"targetPath -> $t")
val entityPath = s"$t/entities"
val relPath = s"$t/relation"
val mapper = new ObjectMapper()
implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset])
implicit val publicationEncoder: Encoder[Publication] = Encoders.kryo(classOf[Publication])
implicit val relationEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
implicit val orpEncoder: Encoder[OtherResearchProduct] = Encoders.kryo(classOf[OtherResearchProduct])
implicit val softwareEncoder: Encoder[Software] = Encoders.kryo(classOf[Software])
log.info("Converting dataset")
val rddDataset =spark.sparkContext.textFile(s"$sourcePath/dataset").map(s => mapper.readValue(s, classOf[OafDataset]))
spark.createDataset(rddDataset).as[OafDataset].write.mode(SaveMode.Overwrite).save(s"$entityPath/dataset")
log.info("Converting publication")
val rddPublication =spark.sparkContext.textFile(s"$sourcePath/publication").map(s => mapper.readValue(s, classOf[Publication]))
spark.createDataset(rddPublication).as[Publication].write.mode(SaveMode.Overwrite).save(s"$entityPath/publication")
log.info("Converting software")
val rddSoftware =spark.sparkContext.textFile(s"$sourcePath/software").map(s => mapper.readValue(s, classOf[Software]))
spark.createDataset(rddSoftware).as[Software].write.mode(SaveMode.Overwrite).save(s"$entityPath/software")
log.info("Converting otherresearchproduct")
val rddOtherResearchProduct =spark.sparkContext.textFile(s"$sourcePath/otherresearchproduct").map(s => mapper.readValue(s, classOf[OtherResearchProduct]))
spark.createDataset(rddOtherResearchProduct).as[OtherResearchProduct].write.mode(SaveMode.Overwrite).save(s"$entityPath/otherresearchproduct")
log.info("Converting Relation")
val rddRelation =spark.sparkContext.textFile(s"$sourcePath/relation").map(s => mapper.readValue(s, classOf[Relation]))
spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath")
}
}

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala
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@ -70,7 +70,7 @@ object SparkCreateInputGraph {
resultObject.foreach { r =>
log.info(s"Make ${r._1} unique")
makeDatasetUnique(s"$targetPath/extracted/${r._1}",s"$targetPath/dedup/${r._1}",spark, r._2)
makeDatasetUnique(s"$targetPath/extracted/${r._1}",s"$targetPath/preprocess/${r._1}",spark, r._2)
}
}

1
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala
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@ -42,6 +42,7 @@ object SparkCreateScholix {
val relationDS: Dataset[(String, Relation)] = spark.read.load(relationPath).as[Relation]
.filter(r => (r.getDataInfo== null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
.map(r => (r.getSource, r))(Encoders.tuple(Encoders.STRING, relEncoder))
val summaryDS: Dataset[(String, ScholixSummary)] = spark.read.load(summaryPath).as[ScholixSummary]

5
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateSummaryObject.scala
View File

@ -1,7 +1,7 @@
package eu.dnetlib.dhp.sx.graph
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Result
import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils
import org.apache.commons.io.IOUtils
@ -29,11 +29,12 @@ object SparkCreateSummaryObject {
log.info(s"targetPath -> $targetPath")
implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result]
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val summaryEncoder:Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
val ds:Dataset[Result] = spark.read.load(s"$sourcePath/*").as[Result]
val ds:Dataset[Result] = spark.read.load(s"$sourcePath/*").as[Result].filter(r=>r.getDataInfo== null || r.getDataInfo.getDeletedbyinference== false)
ds.repartition(6000).map(r => ScholixUtils.resultToSummary(r)).filter(s => s!= null).write.mode(SaveMode.Overwrite).save(targetPath)

106
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkResolveRelation.scala
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@ -1,10 +1,17 @@
package eu.dnetlib.dhp.sx.graph
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Relation, Result}
import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql._
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
@ -25,60 +32,109 @@ object SparkResolveRelation {
val relationPath = parser.get("relationPath")
log.info(s"sourcePath -> $relationPath")
val entityPath = parser.get("entityPath")
log.info(s"targetPath -> $entityPath")
log.info(s"entityPath -> $entityPath")
val workingPath = parser.get("workingPath")
log.info(s"workingPath -> $workingPath")
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
import spark.implicits._
val entities:Dataset[Result] = spark.read.load(s"$entityPath/*").as[Result]
entities.flatMap(e => e.getPid.asScala
.map(p =>
convertPidToDNETIdentifier(p.getValue, p.getQualifier.getClassid))
.filter(s => s!= null)
.map(s => (s,e.getId))
).groupByKey(_._1)
.reduceGroups((x,y) => if (x._2.startsWith("50|doi") || x._2.startsWith("50|pmid")) x else y)
.map(s =>s._2)
.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/resolvedPid")
val rPid:Dataset[(String,String)] = spark.read.load(s"$workingPath/resolvedPid").as[(String,String)]
extractPidResolvedTableFromJsonRDD(spark, entityPath, workingPath)
val mappper = new ObjectMapper()
val rPid:Dataset[(String,String)] = spark.read.load(s"$workingPath/relationResolvedPid").as[(String,String)]
val relationDs:Dataset[(String,Relation)] = spark.read.load(relationPath).as[Relation].map(r => (r.getSource.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_1")), "left").map{
relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_2")), "left").map{
m =>
val sourceResolved = m._2
val currentRelation = m._1._2
if (sourceResolved!=null && sourceResolved._2.nonEmpty)
currentRelation.setSource(sourceResolved._2)
if (sourceResolved!=null && sourceResolved._1!=null && sourceResolved._1.nonEmpty)
currentRelation.setSource(sourceResolved._1)
currentRelation
}.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/resolvedSource")
.save(s"$workingPath/relationResolvedSource")
val relationSourceResolved:Dataset[(String,Relation)] = spark.read.load(s"$workingPath/resolvedSource").as[Relation].map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_1")), "left").map{
val relationSourceResolved:Dataset[(String,Relation)] = spark.read.load(s"$workingPath/relationResolvedSource").as[Relation].map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_2")), "left").map{
m =>
val targetResolved = m._2
val currentRelation = m._1._2
if (targetResolved!=null && targetResolved._2.nonEmpty)
currentRelation.setTarget(targetResolved._2)
if (targetResolved!=null && targetResolved._1.nonEmpty)
currentRelation.setTarget(targetResolved._1)
currentRelation
}.filter(r => r.getSource.startsWith("50")&& r.getTarget.startsWith("50"))
.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/resolvedRelation")
.save(s"$workingPath/relation_resolved")
spark.read.load(s"$workingPath/relation_resolved").as[Relation]
.map(r => mappper.writeValueAsString(r))
.rdd.saveAsTextFile(s"$workingPath/relation", classOf[GzipCodec])
}
private def extractPidsFromRecord(input:String):(String,List[(String,String)]) = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
val id:String = (json \ "id").extract[String]
val result: List[(String,String)] = for {
JObject(pids) <- json \ "pid"
JField("value", JString(pidValue)) <- pids
JField("qualifier", JObject(qualifier)) <- pids
JField("classname", JString(pidType)) <- qualifier
} yield (pidValue, pidType)
(id,result)
}
private def extractPidResolvedTableFromJsonRDD(spark: SparkSession, entityPath: String, workingPath: String) = {
import spark.implicits._
val d: RDD[(String,String)] = spark.sparkContext.textFile(s"$entityPath/*")
.map(i => extractPidsFromRecord(i))
.filter(s => s != null && s._1!= null && s._2!=null && s._2.nonEmpty)
.flatMap{ p =>
p._2.map(pid =>
(p._1, convertPidToDNETIdentifier(pid._1, pid._2))
)
}.filter(r =>r._1 != null || r._2 != null)
spark.createDataset(d)
.groupByKey(_._2)
.reduceGroups((x, y) => if (x._1.startsWith("50|doi") || x._1.startsWith("50|pmid")) x else y)
.map(s => s._2)
.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/relationResolvedPid")
}
/*
This method should be used once we finally convert everythings in Kryo dataset
instead of using rdd of json
*/
private def extractPidResolvedTableFromKryo(spark: SparkSession, entityPath: String, workingPath: String) = {
import spark.implicits._
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
val entities: Dataset[Result] = spark.read.load(s"$entityPath/*").as[Result]
entities.flatMap(e => e.getPid.asScala
.map(p =>
convertPidToDNETIdentifier(p.getValue, p.getQualifier.getClassid))
.filter(s => s != null)
.map(s => (s, e.getId))
).groupByKey(_._1)
.reduceGroups((x, y) => if (x._2.startsWith("50|doi") || x._2.startsWith("50|pmid")) x else y)
.map(s => s._2)
.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/relationResolvedPid")
}
def convertPidToDNETIdentifier(pid:String, pidType: String):String = {
if (pid==null || pid.isEmpty || pidType== null || pidType.isEmpty)

5
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json Normal file
View File

@ -0,0 +1,5 @@
[
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true},
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true}
]

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/config-default.xml → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/extractEntities/oozie_app/config-default.xml
View File

85
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/extractEntities/oozie_app/workflow.xml Normal file
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@ -0,0 +1,85 @@
<workflow-app name="Create Raw Graph Step 1: extract Entities in raw graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the working dir base path</description>
</property>
<property>
<name>targetPath</name>
<description>the graph Raw base path</description>
</property>
</parameters>
<start to="ExtractEntities"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ExtractEntities">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Extract entities in raw graph</name>
<class>eu.dnetlib.dhp.sx.graph.SparkCreateInputGraph</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=2000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
</spark>
<ok to="DropDedupPath"/>
<error to="Kill"/>
</action>
<action name="DropDedupPath">
<fs>
<delete path='${targetPath}/dedup'/>
<mkdir path='${targetPath}/dedup/'/>
</fs>
<ok to="GenerateInputGraphForDedup"/>
<error to="Kill"/>
</action>
<action name="GenerateInputGraphForDedup">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Generate Input Graph for deduplication</name>
<class>eu.dnetlib.dhp.sx.graph.SparkConvertDatasetToJsonRDD</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=3000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn</arg>
<arg>--sourcePath</arg><arg>${targetPath}/preprocess</arg>
<arg>--targetPath</arg><arg>${targetPath}/dedup</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/config-default.xml → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/finalGraph/oozie_app/config-default.xml
View File

51
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/finalGraph/oozie_app/workflow.xml
View File

@ -1,4 +1,4 @@
<workflow-app name="Create Raw Graph Step 1: extract Entities in raw graph" xmlns="uri:oozie:workflow:0.5">
<workflow-app name="Create Scholix final Graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
@ -6,48 +6,22 @@
</property>
<property>
<name>targetPath</name>
<description>the graph Raw base path</description>
<description>the final graph path</description>
</property>
</parameters>
<start to="ExtractEntities"/>
<start to="ImportDatasetEntities"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ExtractEntities">
<action name="ImportDatasetEntities">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Extract entities in raw graph</name>
<class>eu.dnetlib.dhp.sx.graph.SparkCreateInputGraph</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=2000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
</spark>
<ok to="ResolveRelations"/>
<error to="Kill"/>
</action>
<action name="ResolveRelations">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Resolve Relations in raw graph</name>
<class>eu.dnetlib.dhp.sx.graph.SparkResolveRelation</class>
<name>Import JSONRDD to Dataset kryo</name>
<class>eu.dnetlib.dhp.sx.graph.SparkConvertRDDtoDataset</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
@ -60,9 +34,8 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn</arg>
<arg>--relationPath</arg><arg>${targetPath}/extracted/relation</arg>
<arg>--workingPath</arg><arg>${targetPath}/resolved/</arg>
<arg>--entityPath</arg><arg>${targetPath}/dedup</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
</spark>
<ok to="CreateSummaries"/>
<error to="Kill"/>
@ -87,7 +60,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn</arg>
<arg>--sourcePath</arg><arg>${targetPath}/dedup</arg>
<arg>--sourcePath</arg><arg>${targetPath}/entities</arg>
<arg>--targetPath</arg><arg>${targetPath}/provision/summaries</arg>
</spark>
<ok to="CreateScholix"/>
@ -114,7 +87,7 @@
<arg>--master</arg><arg>yarn</arg>
<arg>--summaryPath</arg><arg>${targetPath}/provision/summaries</arg>
<arg>--targetPath</arg><arg>${targetPath}/provision/scholix</arg>
<arg>--relationPath</arg><arg>${targetPath}/resolved/resolvedRelation</arg>
<arg>--relationPath</arg><arg>${targetPath}/relation</arg>
</spark>
<ok to="DropJSONPath"/>
@ -182,9 +155,5 @@
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step3/oozie_app/config-default.xml → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/config-default.xml
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62
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/workflow.xml Normal file
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@ -0,0 +1,62 @@
<workflow-app name="Resolve Relation" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>entityPath</name>
<description>the path of deduplicate Entities</description>
</property>
<property>
<name>relationPath</name>
<description>the path of relation unresolved</description>
</property>
<property>
<name>targetPath</name>
<description>the path of relation unresolved</description>
</property>
</parameters>
<start to="DropRelFolder"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="DropRelFolder">
<fs>
<delete path='${targetPath}/relation'/>
<delete path='${targetPath}/relation_resolved'/>
<delete path='${targetPath}/resolvedSource'/>
<delete path='${targetPath}/resolvedPid'/>
</fs>
<ok to="ResolveRelations"/>
<error to="Kill"/>
</action>
<action name="ResolveRelations">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Resolve Relations in raw graph</name>
<class>eu.dnetlib.dhp.sx.graph.SparkResolveRelation</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=3000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn</arg>
<arg>--relationPath</arg><arg>${relationPath}</arg>
<arg>--workingPath</arg><arg>${targetPath}</arg>
<arg>--entityPath</arg><arg>${entityPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

120
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/workflow.xml
View File

@ -1,120 +0,0 @@
<workflow-app name="Create Raw Graph Step 2: Map XML to OAF Entities" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPath</name>
<description>the working path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
</parameters>
<start to="ExtractDLIPublication"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ExtractDLIPublication">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Extract DLI Entities (Publication)</name>
<class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=5000
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>-e</arg><arg>publication</arg>
</spark>
<ok to="ExtractDLIDataset"/>
<error to="Kill"/>
</action>
<action name="ExtractDLIDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Extract DLI Entities (Dataset)</name>
<class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=5000
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>-e</arg><arg>dataset</arg>
</spark>
<ok to="ExtractDLIUnknown"/>
<error to="Kill"/>
</action>
<action name="ExtractDLIUnknown">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Extract DLI Entities (Unknown)</name>
<class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=5000
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>-e</arg><arg>unknown</arg>
</spark>
<ok to="ExtractDLIRelation"/>
<error to="Kill"/>
</action>
<action name="ExtractDLIRelation">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Extract DLI Entities (Relation)</name>
<class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=5000
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>-e</arg><arg>relation</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

61
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step3/oozie_app/workflow.xml
View File

@ -1,61 +0,0 @@
<workflow-app name="Create Raw Graph Final Step: Construct the Scholexplorer Raw Graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>targetPath</name>
<description>the source path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>entity</name>
<description>the entity to be merged</description>
</property>
</parameters>
<start to="DeleteTargetPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="DeleteTargetPath">
<fs>
<mkdir path="${targetPath}"/>
<delete path='${targetPath}/${entity}'/>
</fs>
<ok to="MergeDLIEntities"/>
<error to="Kill"/>
</action>
<action name="MergeDLIEntities">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Merge ${entity}</name>
<class>eu.dnetlib.dhp.sx.graph.SparkScholexplorerCreateRawGraphJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT}</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/${entity}</arg>
<arg>--targetPath</arg><arg>${targetPath}/${entity}</arg>
<arg>--entity</arg><arg>${entity}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

58
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
View File

@ -1,17 +1,13 @@
package eu.dnetlib.dhp.oa.graph.raw;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.Mockito.lenient;
import java.io.IOException;
import java.util.List;
import java.util.Optional;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.junit.jupiter.api.BeforeEach;
@ -20,22 +16,12 @@ import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.IOException;
import java.util.List;
import java.util.Optional;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Instance;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.lenient;
@ExtendWith(MockitoExtension.class)
public class MappersTest {
@ -74,7 +60,7 @@ public class MappersTest {
assertValidId(p.getId());
assertEquals(1, p.getOriginalId().size());
assertEquals(2, p.getOriginalId().size());
assertTrue(p.getOriginalId().contains("10.3897/oneeco.2.e13718"));
assertValidId(p.getCollectedfrom().get(0).getKey());
@ -261,8 +247,8 @@ public class MappersTest {
final Relation r2 = (Relation) list.get(2);
assertValidId(d.getId());
assertEquals(1, d.getOriginalId().size());
assertTrue(d.getOriginalId().contains("oai:zenodo.org:3234526"));
assertEquals(2, d.getOriginalId().size());
assertTrue(d.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:zenodo.org:3234526")));
assertValidId(d.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
assertTrue(d.getAuthor().size() > 0);
@ -351,8 +337,11 @@ public class MappersTest {
final Publication p = (Publication) list.get(0);
assertValidId(p.getId());
assertTrue(p.getOriginalId().size() == 1);
assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0));
assertEquals(2, p.getOriginalId().size());
assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:pub.uni-bielefeld.de:2949739")));
//assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0));
assertValidId(p.getCollectedfrom().get(0).getKey());
assertTrue(p.getAuthor().size() > 0);
@ -413,7 +402,8 @@ public class MappersTest {
assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, d.getDataInfo().getProvenanceaction().getSchemename());
assertValidId(d.getId());
assertTrue(d.getOriginalId().size() == 1);
assertEquals(2, d.getOriginalId().size());
assertEquals("feabb67c-1fd1-423b-aec6-606d04ce53c6", d.getOriginalId().get(0));
assertValidId(d.getCollectedfrom().get(0).getKey());
@ -663,8 +653,8 @@ public class MappersTest {
final Dataset p = (Dataset) list.get(0);
assertValidId(p.getId());
assertTrue(p.getOriginalId().size() == 1);
assertEquals("df76e73f-0483-49a4-a9bb-63f2f985574a", p.getOriginalId().get(0));
assertEquals(2, p.getOriginalId().size());
assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("df76e73f-0483-49a4-a9bb-63f2f985574a")));
assertValidId(p.getCollectedfrom().get(0).getKey());
assertTrue(p.getAuthor().size() > 0);